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A configurational interpretation of the axial phosphate spacing in polynucleotide helices and random coils

1976; Wiley; Volume: 15; Issue: 12 Linguagem: Inglês

10.1002/bip.1976.360151207

1097-0282

Wilma K. Olson, Gerald S. Manning,

RNA Interference and Gene Delivery

Abstract The structural implications arising from the observation (set forth in the preceding paper) that the charge density of a single‐stranded randomly coiling polynucleotide chain is approximately equal to that of one strand of the familiar double helix are here examined. A computational scheme is described to obtain (using bond lengths, valence bond angles, and internal rotation angles) the mean phosphate–phosphate spacing parameter b along the chain axes of any single‐stranded polynucleotide molecule. Attention is then focused upon the computed interphosphate spacing associated with both the theoretical randomly coiling polynucleotide that reproduces the observed experimental unperturbed dimensions and the familiar single‐stranded helix. The calculations clearly demonstrate that the parameter b only weakly reflects the spatial configuration of the chain. The approximate equivalence of the b values associated with the single‐stranded helix and the unperturbed randomly coiling polynucleotide is not indicative of strong configurational similarities between the two forms. The familiar helix is composed of a sequence of identically conformed compact structural residues while the random coil is characterized by a variety of chain‐repeating residues of which a large proportion are extended units.